He stayed
by sebisurf
Summary: What if Anakin stayed at the temple, and Windu lost his duel with Palpatine? How would order 66 play out, with Anakin defending the temple instead of attacking it? Find out inside!
1. Chapter 1

**Author's note: Hi, so this is the first story i've ever published, anywhere. Honestly i'm not even sure what i'm doing so please try to be gentle with the criticism (though I still encourage it because I want to get better at writing). Also i wrote this rather more rushed than i would've liked but i really wanted to publish something to kinda see what other people thought of my writing (besides my sister and a few friends) and also because I have a huge star wars obsession right now to the point where i couldn't study or focus on anything else, because of all the stories and ideas i have in my head. Also if anybody is interested in beta reading this story that would also be great. Ok that kinda got long haha**

 **Disclaimer: Not entirely sure why people put this in a fan fiction site but here goes... I own nothing in this story.**

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Anakin sat silently in the Jedi Temple, trying to meditate.

He was never much good at meditating but he found himself anxious and with little else to do as he waited for news of Master Windu's arrest of Chancellor Palpatine. _Palpatine._ The very name evoked rage inside the young Jedi Knight. He deceived them all, HE was the cause of this terrible war. Still, what most frightened Anakin was Palpatine's voice in his head:

 _If the jedi destroy me, you will lose any chance of saving her…_

Her. Padme. His wife, carrying his child! His world. He can't lose her, he wouldn't be able to bear losing someone else he cared about. Like he lost master Qui-Gon or his padawan, Ahsoka… Like he lost his mother.

Palpatine said he had the power to save her, that he could teach this power to him but how could he know this was the truth? After all the lies the _Sith Lord_ had fed everyone, even master Yoda had not seen through the lies, or felt his presence before! No, he couldn't be trusted. Master Windu was right, Anakin couldn't face Palpatine, and he couldn't clearly decide what to do if he did, not to mention he was in nowhere near focused enough to face a Sith Lord right now. _Huh, caution. Maybe some of Obi-Wan's lessons really did reach me._ Anakin smiled at the thought of his old mentor and best friend, the only one in the Jedi Council who truly seemed to trust him.

Then he remembered his friend's situation in Utupau, and decided to see if he could find any updates as to Obi-Wan's status. As he started to walk across a hallway which overlooked the entrance to the Jedi Temple, a very powerful and terrible tremor in the force hit him and he felt as all the air escaped his lung. A freezing cold chill ran up his spine. He felt a presence, a pure dark side entity more powerful than he could've ever imagined. Terror dawned on him as he realized, _Master Windu is dead, and he has failed_.

Suddenly he heard steps, no, _marching,_ he looked down at the steps of the Jedi Temple as he saw the 501st, his own legion of clone troopers, following a dark hooded figure. No, how had he failed to feel it, how had he fail to sense master Windu's defeat earlier?! How strong could this monster be that he hid his signature all that time?

Anakin looked on hopelessly as he saw Master Jurokk, the temple's gatekeeper bravely approach the dark lord with two temple guards flanking him, lightsabers ignited. "What's going on here? Chancellor? Is that you?" Anakin barely made out what master Jurrok said when suddenly the cloaked figure extended his hands and used force lightning to shock the jedi master and guards to death while cackling loudly and yelling: "KILL THEM ALL! HAHAHA".

As he saw this, Anakin let out a deafening "NOOO!" and Palpatine increased the intensity of his sick laugh, the clone troopers now rushing inside the temple and shooting anything that moved. Anakin ran down the hallways and corridors until he reached an opening and saw that it was too late, the jedi were being overwhelmed, most still shocked at what was happening, then he heard many boots halting to a stop in unison, looked ahead and saw a squad of clone troopers, _his_ clone troopers starting to aim their blasters at him. "Stop! I'm ordering you to stop! It's me! General Skywalker, your commander! Remember!?" Anakin desperately said. The trooper's faltered for a moment as if realizing what they were doing. Then, as if snapping into a trance, they trained their weapons on him again. "Good soldiers follow orders" said the squad leader before giving the order to fire.

Anakin's force-enhanced reflexes are all that saved him as his mind flashed back to clone trooper Tup, killing jedi master Tiplar; and the ensuing chaos that followed leading to Tup, and Fives' deaths. Fives was saying the truth, the chancellor did manipulate the cloning process, this is what he tried to warn them about. By now, Anakin outright hated Palpatine and wanted nothing more than to kill him.

Anakin used his newfound rage to ignore the pain of killing his former soldiers. He searched his feelings in order to find Palpatine and moved as a machine annihilating any clone in his way, cutting a path straight to the sith lord. He didn't notice as many jedi were now composing themselves and rallying behind the young jedi knight inspired by his brave push against the clones.

As he reached Palpatine, he saw him in a saber lock with both lightsabers, one against master Cin Drallic, and the other against Serra Keto, while master Shaak Ti charged at him from behind. Palpatine simply laughed as he unleashed a force repulse which pushed away the three masters. Then he turned his head in Anakin's direction and grimaced in annoyance at the small army of jedi that followed him. He looked up and collapsed the archway they were passing under with the force. Anakin was able to jump out of the way and pull a jedi padawan that was next to him just in time to avoid the debris, but the rest of his small army was not so lucky. Half had been crushed and the other half was trapped on the other side with clones still pouring in. He looked at who he saved, a young blue twi'lek boy who he had recently given some lightsaber lessons. He knew the boy was strong in the force but not the most talented when it came to lightsabers and felt a little proud that perhaps Anakin's lessons had helped the boy survive so far.

"You okay, Zanat?" Anakin asked the boy while smiling a bit to try and comfort him.

Zanat grinned brightly, his hero and role model had just saved him! "Master Skywalker! Thank yo-" suddenly Zanat gasped and clutched at his throat as he was lifted of the ground and in two seconds his neck snapped. Anakin's look of horror morphed into one of pure hatred as he looked at Palpatine.

"MONSTER!" Anakin screamed at the top of his lungs as he noticed Palpatine had just impaled Serra Keto and what was left of Cin Drallic was a burned corpse, mangled by force lightning. Shaak Ti was standing in front of the doors to the council chamber no longer appearing calm and resolved as usual for her, but now appearing desperate. "Anakin we must not let him reach the younglings." Then Anakin felt it, a large group of younglings hiding in the council chamber. He stood up with an expression of pure determination in his face. "I WILL kill you, Palpatine." Laughter erupted once again from the corrupted chancellor. "My dear boy, Palpatine is a fictional character, my name is Darth SIDIOUS!" Palpatine placed a serious and deadly tone to the last two words.

Both jedi charged Darth Sidious at the same time, he simply grinned and force pushed Shaak Ti and focused on Anakin. The three lightsabers flashed at inhuman speeds as Anakin seemed impossibly focused, and pushed Sidious, even forcing him on the defensive. Each time Sidious attempted to mount an offensive Anakin quickly countered and continued his assault, showcasing his incredible mastery of Djem So. Despite being on the defensive, Sidious simply chuckled and continued taunting Anakin.

"Yess," Sidious hissed. "use your hatred, let it fill you with strength, feel the power of the dark side flow through you." Anakin's speed and viciousness only increased with each word.

Shaak Ti slowly regained consciousness and was amazed at the spectacle of lightsaber combat she witnessed before she decided she needed to join. She used the force to fling a piece of debris at Sidious, who was able to catch it with the force through his left hand but was enough to distract him from Anakin for a brief second. Anakin came down with a hard two-handed cleave, and Sidious was just barely able to block it in time with his free hand. However Anakin was able to slide down his blade and actually burn Palpatine's fingers as well as damage the lightsaber, rendering it useless. Sidious howled inhumanly in pain and dropped the saber as he force jumped well out of range of Skywalker, but just in range of master Shaak Ti. She engaged Sidious who was not as accustomed to using his left hand only and was not able to dispatch her as quickly as he would've liked. Anakin attempted to join with a leaping attack but Sidious saw this and intercepted him midair, kicking him into a wall.

Anakin's head throbbed. Ever since he had given in to his hatred he felt more powerful than ever before. He could see clearly what his opponent was going to do before he did it, and he barely even had to tell his body what to do, it **knew** what to do. Was this the power of the dark side? It almost felt like when he defeated Dooku. He had used his anger that time, but in a controlled manner, right now he was in a state of utter frenzy. And the result was him feeling ten times stronger than he ever had before! If this is the dark side's power, perhaps the jedi **are** wrong and they should study it. He would have to entertain those thoughts further on a later date, **after** he killed Sidious.

As his vision cleared, he saw Sidious overpowering Shaak Ti. He disarmed her and raised his lightsaber for the killing blow, laughing.

"NO!" Anakin reached through the force and pulled Sidious away and straight into the rubble of the archway that was brought down earlier. As Sidious stood with a growl on his face, truly angered for the first time in the fight, he pulled Anakin's lightsaber away from him before he'd even realized he'd dropped it and unleashed a barrage of force lightning. However Anakin was somehow using the force to block it and…

The Sith Lord couldn't believe it but it seemed either Anakin was redirecting Sidious's force lightning, or he was producing his own as Sidious felt the familiar burning sensation and screamed in anger and agony. However, Skywalker seemed to be suffering as well as he too was screaming in his great effort.

Suddenly Anakin turned to Shaak Ti and she gasped when she saw his eyes were yellow, but were returning to their warm blue color, as he gave her pleading look.

"Go! Take the younglings and get as far away from here as you can!" Anakin looked desperate as he struggled to keep Sidious at bay.

"But Anakin,"

"Please!" Anakin cut her off, and she nodded sadly, knowing the great sacrifice he was making.

She entered the council chamber and quickly ushered the younglings to follow her past Anakin, towards a secret emergency shuttle, on the way she encountered some clone troopers but easily dispatched them and finally reached the shuttle and punched in random coordinates to take her somewhere far away from the republic. As the ship was taking off she felt a huge tremor in the force and as she looked back she saw there had been a huge explosion in the section where Anakin and Darth Sidious where dueling.

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 **A/N Okey obviously that's not really an ending, but i really want to know what people think of this small chapter before continuing, which btw i already have the rest of this story roughly planned out and in fact i have a bunch of other ideas i could do with the new alternate timeline i create in this story so let me know if anyone's interested, heck even if i only have one reviewer who encouraged me to continue i probably would haha**


	2. Chapter 2

**A/N: I AM SOOO SORRY I took so long updating. I told a lot of you guys I would update weeks ago so I'm terribly sorry for not keeping my word. I just got bogged down with finals, and Senior Year stuff, track team stuff, college stuff, my laptops giving problems, and also i admit, a bit of laziness on my part. It also got kinda hard for me to write because i actually did almost like a 180 on what i was originally gonna do in this story. Partly because I heard what you guys were saying and i felt that many of you would be disappointed with the original ending which after reviewing it felt almost even lazy to me, besides the original ending would've been like half this chapter and it felt crappy to make you guys wait so long for something short and maybe not as entertaining. Still if anyone's curious i'd be happy to tell them what my original idea was through pm. Also a side effect of the changes is that while this was originally like a one or twoshot now it'll probably extend a few more chapters. Finally THHANK YOU ALL 4 THE AWESOME FEEDBACK it was much more positive than i hoped for and for that i'm really grateful and i hope you like this chapter as well.**

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 **Chapter** **2**

Tears streamed down Padme's face as she saw the smoke emanating from the Jedi temple. All over the holonet reports flashed of the Jedi's "betrayal" and alleged assassination attempt against the chancellor. It had to be a lie. She knew many jedi, they were some of the most loyal friends she'd ever had, not to mention her husband was a jedi himself.

 _Anakin…_ The father of her unborn child. She couldn't lose him, especially not now when it seemed they might finally be able to enjoy the peace they had both fought so hard for, the war was nearly over!

 _Ani please… come back to me._

Suddenly another huge explosion rocked the temple, somehow though, this one seemed different from the others. Padme sank to the floor in tears as fear gripped her heart.

 **Jedi Temple**

Palpatine slowly rose from the rubble. He and Anakin had been in a force lock that ended in a huge explosion which leveled half the temple and obliterated any living being caught in its radius, aside from himself and Anakin. His face and body was left horribly scarred after his duel with the Chosen One, who was still lying unconscious several feet away. The sith lord moved toward the broken body of Skywalker to check on him. Anakin's robes were half-destroyed, leaving his chest and part of his abdomen, now even more scarred than before, exposed. He was barely alive. Even though he now felt a great hate towards the boy for defying his plans, Sidious was not yet finished with him and therefore used the force to help keep Anakin alive until a rescue team of clone troopers arrived along with Palpatine's political advisors.

"Take me to the senate, I must address the people personally before any wild rumors start. I shall inform them of the Jedi's betrayal and our reorganization into a galactic **empire**." Palpatine smiled as he spoke the last statement. His advisors nodded avoiding the new and frightening appearance of their new emperor.

"Sir, what should we do with General Skywalker?" a clone trooper cautiously inquired.

"Take him to Kamino, I have plans for him." Sidious turned and looked straight at the trooper, "Keep him alive, however make his journey and stay there as unpleasant as possible, he will suffer for his insolence!" -Then he stared straight at Anakin who was lying in a medical pod-"I will not be denied an apprentice, Skywalker."

 **On Board Bail Organa's ambassador ship**

Obi-Wan sat in Senator Organa's ship, meditating on what he just learned and preparing himself for what he might find when he arrives on what's left of the Jedi temple. So many Jedi dead. So many friends, brothers, sisters… How could this have happened? How had they been so blind? He had so many questions yet he wasn't entirely sure he was ready to hear the answers. He wondered if Anakin had made it. Based on the reports in the holonet and what Bail told Yoda and him, it seemed unlikely anyone had made it. However, they didn't know Anakin like he did, his former padawan was very resourceful, surely he must've found a way to survive. Then his thoughts drifted to Ahsoka. He feared Anakin and himself may have doomed her by giving her half the 501st to aide her campaign on Mandalore to capture Maul. While in the past he would've denied Rex would ever betray Anakin or Ahsoka, after being shot at as if he was just another droid by his own troops Obi-Wan held little hope the same didn't happen to Ahsoka.

His train of thoughts was interrupted by a protocol droid entering his room.

"Master Kenobi, Senator Organa requests your presence immediately."

"What's going on?" Obi-Wan asked as he stood up.

"It seems we've intercepted a message from another jedi survivor."

"Who?"

"I don't know, I suggest you hurry though if you wish to find out." The droid motioned for Kenobi to leave the room.

"Very well" Obi-Wan responded making a face at the slightly sassy droid.

When he entered the room he found Yoda and Bail Organa speaking to the hologram of none other than Shaak Ti. He knew she was in coruscant when they were betrayed, she would be able to tell them exactly what happened. "Shaak Ti are you alright? Is anyone else there with you?" Kenobi addressed her as he hurried to the holoterminal.

"Yes, I'm alright master Kenobi, and I have a group of younglings here with me."-Shaak Ti quickly assured-"However, I'm afraid the Jedi Temple has been destroyed. I believe a few others were able to escape as well but I don't know who or how many. I believe I am also the only Master to have made it out."

"Who could've done this? And What of Anakin?" Obi-Wan questioned with a slight tremble in his voice.

Shaak Ti sighed as she began to recount what had happened. How Anakin had discovered the chancellor was the mysterious sith lord they had been searching for since the war started. How Master Windu charged her with the protection of the jedi temple and left with three more masters to capture lord 'Sidious', as the discovered sith had called himself. It seemed Windu's jedi strike team had failed to capture Palpatine, for later in the night the dark lord marched up the Jedi Temple steps flanked by an army of clones as they mercilessly purged the jedi at the temple.

As she relayed her story, Shaak Ti felt a pang in her heart as she realized she had utterly failed her duty to protect the temple and even worse, she realized she could've avoided this disaster. Her thoughts went back to the incident that occurred with clone trooper fives. This is the conspiracy he had tried to warn them about. Those biochips, that's how Palpatine was able to take control of the army and convinced them to betray the jedi.

"Shaak Ti… What happened to Anakin?" Obi-Wan slowly pleaded for her to continue.

She decided that it didn't matter anymore, the past couldn't be changed therefore she should no longer dwell in it. "Right, yes, apologies master Kenobi I guess I'm still in shock after all of the events that have recently transpired."-Obi-Wan nodded sympathetically-"As I was saying, the dark lord's power is unlike anything I have ever seen or felt before. He cut down masters as if they were younglings, and he killed younglings as if they were animals."-Shaak Ti felt tears start to well up in her eyes and a lump forming in her throat but she pushed it back in order to continue-"He seemed unstoppable and tee clones were too many, Master Cin Drallic, his old padawan Serra Keto, and myself made a last stand in order to protect the remaining younglings and cover the escape for a few other jedi. However we were completely outmatched, that is until Skywalker arrived. He had remained in the temple as well under Master Windu's orders..." She continued to narrate how Anakin bravely stood up to Darth Sidious and saved her many times, however she left out the fact he used the dark side in order to do this as she deemed it unnecessary.

"…After the explosion I no longer felt Anakin's signature"-She looked sadly at Obi-Wan, who lowered his head and averted his gaze-"However Palpatine's signature was only slightly weakened which leads me to fear the worst has happened and our enemy is still alive and well."

She looked at the small figure to Obi-Wan's right. Yoda had his eyes closed throughout her story as he seemed to ponder deeply. He opened them and said: "To Tython, you must go, to the first Jedi Temple. Take the younglings you have rescued with you. Some much needed clarity on how we should continue, the birth place of our order may bring us. To Coruscant, master Kenobi and I will go. Disable the transmission that calls surviving jedi to the temple, we must."

"Understood, master" Shaak Ti bowed and her hologram faded.

A soldier came up to Organa and spoke: "Sir, the supreme chancellor will be addressing the senate in a few hours. He requests your presence." Bail looked to Yoda, who nodded in approval. "Tell him I'll be there." He told the soldier, who promptly nodded and walked away. "It could be a trap, lure all the senators in one place in order to take them out and consolidate his power."

"Unlikely,"-Obi-Wan spoke as he finally looked up even though he still held a distraught look on his face-"Palpatine still needs the senate in order to maintain control over the many different systems."

"Agree with Obi-Wan, I do. Besides, a nice distraction it will be. Easier for us"-Yoda motioned to Obi-Wan and himself-"to enter the temple."

"Then let us make haste to Coruscant" Organa finished.

 **Back at the ruins of the Jedi Temple**

Yoda and Obi-Wan finished dispatching the relatively few clones left at the temple easily and proceeded to the communications tower. On the way they couldn't help but notice the carnage left behind in the wake of the disaster that occurred the night before. Bodies of jedi and clones littered every walkway and passage. Even younglings were among the bodies. Obi-Wan recited the Jedi code in his head over and over in order to keep himself calm and avoid breaking down in either anger or sadness. Yoda simply reminded him that they were now ones with the force. After they arrived at the com tower and he had recalibrated the transmission, Obi-Wan went to the holorecordings of the night before to see if he could find out whether Anakin had really died or not.

"Let go of your pain, do not seek more pain than is necessary." Yoda attempted to save Obi Wan from further suffering.

"I must see him." Obi Wan responded determined.

As the recording of Anakin's duel with Sidious finished, he realized where exactly it had taken place and rushed off to see if he could find his best friend's body at least. Yoda followed silently shaking his head in sadness. He reached the spot and sure enough it seemed to be the epicenter of the great force blast Shaak Ti described and the one that ended the recording. He started searching through the debris, almost like a madman looking for some ancient treasure. Yoda just looked on in silence. Obi Wan continued like this until finally he spotted something familiar: Anakin's lightsaber. His hands trembled as he reached for it. When he finally held it in his hands, the jedi master finally broke down and tears fell from his face on to the lightsaber.

Yoda simply meditated. The more he focused, the less sure he was The Chosen One was truly dead. However, he decided best not to mention it to Obi Wan for he couldn't say with certainty Anakin was alive, and right now would not be the best time to further confuse Obi Wan who was now struggling to maintain his composure.

 **Senate Room**

Padme managed to compose herself enough to attend the supreme chancellor's convocation of the senate, and now sat in her assigned seat in the senate room listening in horror as the, now horribly scarred, chancellor claimed the jedi had betrayed the republic and attempted to assassinate him. Padme was now more afraid than ever however she didn't let I show, she couldn't, she had to be strong now. As the chancellor continued his speech, senator Organa arrived.

"What's happened?" Bail asked as he sat down next to her.

"The chancellor's been elaborating on a plot by the jedi to overthrow the senate." She noticed Organa had a very suspicious look on his face. At first she feared it to be because he had noticed the fear in her voice, which she tried to hide the best she could. But then she noticed he was actually laser focused on Palpatine, almost as if he was glaring at him.

"-The remaining jedi will be hunted down and defeated!" Applause filled the room while Padme gasped, whispering: _Anakin_. She needed to find him and know he was ok.

"The attempt on my life has left me scarred and deformed."

She felt like crying like a little girl right then and there, but she knew it was useless and besides no one could know why she felt like this.

"But I assure you, my resolve has never been stronger!"

Even if Anakin had… passed, their relationship had to be kept a secret or else she would lose her position as senator of Naboo and her child would be in grave danger.

"In order to ensure security and continuing stability,"-Palpatine begins raising his voice-"the republic shall be reorganized into The FIRST GALACTIC EMPIRE!" the room roars in applause as the chancellor raises his hands.

"So this is how liberty dies, with thunderous applause." Padme states, visibly appalled by what she is witnessing and shares a fearful look with Bail Organa.

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 **A/N: ok so next chapter I'm hoping to touch on Ahsoka as well, and what's next for Anakin. (If you haven't guessed by now i'll give you a hint, Kamino is where the clone army is made) also i'm thinking of bringing an oc into this story (he wouldn't be a MAJOR character but i would try my best to characterize him as well as i can, and he'd probably be a love interest for ahsoka) but then again maybe i'll write a separate fic for that.**


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